Cobalt in PDB 8bmy: Bacteroides Thetaiotaomicron Surface Lipoprotein Bound to Cyanocobalamin

The structure of Bacteroides Thetaiotaomicron Surface Lipoprotein Bound to Cyanocobalamin, PDB code: 8bmy was solved by J.Abellon-Ruiz, K.Jana, A.Silale, A.Basle, U.Kleinekathofer, B.Van Denberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.07 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.315, 59.078, 101.544, 90, 103.87, 90
R / Rfree (%)	17.9 / 22.3

The structure of Bacteroides Thetaiotaomicron Surface Lipoprotein Bound to Cyanocobalamin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cobalt atom in the Bacteroides Thetaiotaomicron Surface Lipoprotein Bound to Cyanocobalamin (pdb code 8bmy). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Bacteroides Thetaiotaomicron Surface Lipoprotein Bound to Cyanocobalamin, PDB code: 8bmy:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Bacteroides Thetaiotaomicron Surface Lipoprotein Bound to Cyanocobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Bacteroides Thetaiotaomicron Surface Lipoprotein Bound to Cyanocobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:14.2 occ:1.00 CO A:CNC401 0.0 14.2 1.0 C1A A:CNC401 1.8 17.2 1.0 N21 A:CNC401 1.8 14.1 1.0 N24 A:CNC401 1.9 14.4 1.0 N23 A:CNC401 1.9 13.3 1.0 N22 A:CNC401 1.9 14.8 1.0 N3B A:CNC401 2.2 14.5 1.0 C19 A:CNC401 2.7 15.5 1.0 C9 A:CNC401 2.8 14.7 1.0 C1 A:CNC401 2.8 14.6 1.0 C14 A:CNC401 2.9 13.9 1.0 C11 A:CNC401 2.9 14.1 1.0 C4 A:CNC401 2.9 14.0 1.0 C16 A:CNC401 2.9 13.3 1.0 N1A A:CNC401 2.9 18.8 1.0 C6 A:CNC401 3.0 15.0 1.0 C2B A:CNC401 3.1 15.9 1.0 H2B A:CNC401 3.2 15.5 1.0 C10 A:CNC401 3.2 12.7 1.0 C9B A:CNC401 3.2 15.4 1.0 C15 A:CNC401 3.3 13.7 1.0 H201 A:CNC401 3.3 15.2 1.0 C5 A:CNC401 3.4 14.1 1.0 H4B A:CNC401 3.6 16.3 1.0 C20 A:CNC401 3.6 15.1 1.0 C4B A:CNC401 3.9 16.4 1.0 H203 A:CNC401 3.9 15.0 1.0 H371 A:CNC401 4.1 16.2 1.0 C2 A:CNC401 4.1 14.2 1.0 H261 A:CNC401 4.1 13.8 1.0 C18 A:CNC401 4.1 14.2 1.0 C3 A:CNC401 4.2 14.6 1.0 C8 A:CNC401 4.2 15.1 1.0 H10 A:CNC401 4.2 13.3 1.0 C13 A:CNC401 4.2 15.0 1.0 C12 A:CNC401 4.2 15.8 1.0 C17 A:CNC401 4.2 13.7 1.0 C7 A:CNC401 4.2 15.7 1.0 N1B A:CNC401 4.3 17.1 1.0 H542 A:CNC401 4.4 13.0 1.0 H18 A:CNC401 4.4 14.4 1.0 C8B A:CNC401 4.4 16.9 1.0 H202 A:CNC401 4.4 14.9 1.0 H471 A:CNC401 4.5 15.3 1.0 H412 A:CNC401 4.6 16.4 1.0 C26 A:CNC401 4.6 13.7 1.0 H421 A:CNC401 4.6 17.7 1.0 HZ2 A:TRP272 4.6 15.9 1.0 C37 A:CNC401 4.7 16.4 1.0 H3 A:CNC401 4.7 14.3 1.0 H262 A:CNC401 4.7 13.7 1.0 H481 A:CNC401 4.8 17.9 1.0 C53 A:CNC401 4.8 14.0 1.0 C41 A:CNC401 4.8 16.4 1.0 H13 A:CNC401 4.8 15.1 1.0 C35 A:CNC401 4.9 15.5 1.0 H8 A:CNC401 4.9 15.3 1.0 C54 A:CNC401 4.9 12.7 1.0 C47 A:CNC401 4.9 15.3 1.0 H561 A:CNC401 4.9 13.5 1.0 HH2 A:TRP272 4.9 18.0 1.0 HH2 A:TRP194 5.0 12.2 1.0 C48 A:CNC401 5.0 18.0 1.0

Cobalt binding site 2 out of 2 in the Bacteroides Thetaiotaomicron Surface Lipoprotein Bound to Cyanocobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Bacteroides Thetaiotaomicron Surface Lipoprotein Bound to Cyanocobalamin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:15.0 occ:1.00 CO B:CNC401 0.0 15.0 1.0 C1A B:CNC401 1.8 17.1 1.0 N23 B:CNC401 1.8 13.9 1.0 N21 B:CNC401 1.8 12.7 1.0 N24 B:CNC401 1.8 14.1 1.0 N22 B:CNC401 1.9 13.8 1.0 N3B B:CNC401 2.2 14.9 1.0 C19 B:CNC401 2.7 14.5 1.0 C9 B:CNC401 2.8 13.5 1.0 C1 B:CNC401 2.8 13.9 1.0 C14 B:CNC401 2.8 13.5 1.0 C11 B:CNC401 2.8 15.9 1.0 C4 B:CNC401 2.8 12.9 1.0 C6 B:CNC401 2.9 14.3 1.0 C16 B:CNC401 2.9 13.3 1.0 N1A B:CNC401 2.9 18.9 1.0 C2B B:CNC401 3.1 16.0 1.0 C10 B:CNC401 3.2 15.1 1.0 H2B B:CNC401 3.2 16.1 1.0 C9B B:CNC401 3.3 15.1 1.0 H201 B:CNC401 3.3 13.7 1.0 C15 B:CNC401 3.3 12.7 1.0 C5 B:CNC401 3.3 13.7 1.0 H4B B:CNC401 3.5 15.8 1.0 C20 B:CNC401 3.5 13.5 1.0 H203 B:CNC401 3.8 13.5 1.0 C4B B:CNC401 3.8 16.0 1.0 C2 B:CNC401 4.1 13.9 1.0 H261 B:CNC401 4.1 14.5 1.0 C18 B:CNC401 4.1 13.4 1.0 H371 B:CNC401 4.1 14.3 1.0 C3 B:CNC401 4.1 14.7 1.0 C13 B:CNC401 4.1 15.1 1.0 C8 B:CNC401 4.2 13.7 1.0 C12 B:CNC401 4.2 15.8 1.0 H10 B:CNC401 4.2 14.8 1.0 C7 B:CNC401 4.2 14.8 1.0 C17 B:CNC401 4.2 13.9 1.0 N1B B:CNC401 4.3 17.6 1.0 H18 B:CNC401 4.4 13.5 1.0 H202 B:CNC401 4.4 13.8 1.0 H542 B:CNC401 4.4 14.0 1.0 C8B B:CNC401 4.5 16.1 1.0 H471 B:CNC401 4.5 16.5 1.0 C26 B:CNC401 4.5 14.8 1.0 HZ2 B:TRP272 4.6 15.7 1.0 H421 B:CNC401 4.6 15.4 1.0 H412 B:CNC401 4.7 14.5 1.0 C37 B:CNC401 4.7 14.6 1.0 H3 B:CNC401 4.7 14.6 1.0 H262 B:CNC401 4.7 14.5 1.0 H13 B:CNC401 4.8 15.7 1.0 C35 B:CNC401 4.8 13.7 1.0 H481 B:CNC401 4.8 18.0 1.0 C53 B:CNC401 4.8 14.6 1.0 H8 B:CNC401 4.8 14.0 1.0 C47 B:CNC401 4.9 16.5 1.0 C41 B:CNC401 4.9 14.7 1.0 HH2 B:TRP272 4.9 15.9 1.0 H561 B:CNC401 4.9 14.5 1.0 C54 B:CNC401 4.9 14.0 1.0 H302 B:CNC401 5.0 15.3 1.0 HH2 B:TRP194 5.0 12.1 1.0 C48 B:CNC401 5.0 17.9 1.0

J.Abellon-Ruiz, K.Jana, A.Silale, A.M.Frey, A.Basle, M.Trost, U.Kleinekathofer, B.Van Den Berg. Btub Tonb-Dependent Transporters and Btug Surface Lipoproteins Form Stable Complexes For Vitamin B 12 Uptake in Gut Bacteroides. Nat Commun V. 14 4714 2023.
ISSN: ESSN 2041-1723
PubMed: 37543597
DOI: 10.1038/S41467-023-40427-2